It appears that Solid Snake has successfully infiltrated and bugged LittleBigPlanet; users at PS3Fanboy.com have reported that in combination with the latest title update, using the MGS packs somehow winds up deleting progress and user-created content.

According to this forum post, random things will go missing from one's save. For example, progress in the MGS4 level pack may disappear.

Fortunately, some PS3F commentators seem to have the solution...click "Read More" for the source link and quotes.

Just delete some of the community objects or photos you have in Creation-Mode.

After that no progress will be lost.

...it seems this bug is due to the profile size allotted to each player. Profile size is determined by how many stickers, costumes etc you have in your pop it...what happens is when you too many community objects stickers and my objects....you feel (sic) up the amount of space you were allotted by Mm. If you simply delete the community objects and stickers that you don't need and keep your My photos and objects to necessity minimum the game saves everything just fine.
The MGS added many objects to our pop its...most of us had a ton of community and personal objects/stickers in our profile already...

Just go into your level and delete ALOT of community items. I deleted about 47 of them and it started to save again.

Given Media Molecule's track record so far, it's safe to assume that this will be fixed quite soon. But for now, be extra careful...don't create levels without reading the comments above, don't eat the yellow snow, and stay away from the walls - I think that about covers it.